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Determining typical interatomic distances for hydrogen bonds in a lithium sulfate hydrate. Removing all van der Waals contacts from the adjacency matrix.
Algorithm:
1. Open a Crystal Data window for a lithium sulfate hydrate (Ref. Code 22347) with all allocated hydrogen atoms (Compound/Edit or double left click or click F4).
2. Open Adjacency matrix tab and find all hydrogen bonds (H) in the list. Find typical interatomic distances for the hydrogen bonds O-H…O. What range do they vary in? (see the values of R in Å)
3. Find all contacts H…O corresponding to Van der Waals bonding. What are their distances?
4. Remove all the "non H" H…O contacts using local menu (Delete Selected or Change Type/No bond commands). Save the changes. Pay attention that the Reference Code field contains the Collection Code of the structure in ICSD.
5. Open a Crystal Data window for a lithium sulfate hydrate without allocated hydrogen atoms. Look at the typical interatomic distances corresponding to O…O hydrogen bonds. For example, compound with Ref. Code 18173 shows O1…O5 2.870 Å vdW
6. If instead of going on Change Type (step 4 above) you click on Information, you will get, e.g. for structures 22347 (with H, left) and 18173 (without H, right) the following self-explanatory windows:
Exercise:
Perform the algorithm for lithium selenate hydrates. Are there any differences in interatomic distances O…O for hydrogen bonds in lithium sulfate and selenate hydrates?
Answer:
The distances O…O for hydrogen bonds in lithium selenate is 2.87 Å 3.00-2.881 Å are typical ranges for O…O distances in hydrogen bonds in lithium sulfate.
Algorithm:
1. Open a Crystal Data window for a lithium sulfate hydrate (Ref. Code 22347) with all allocated hydrogen atoms (Compound/Edit or double left click or click F4).
2. Open Adjacency matrix tab and find all hydrogen bonds (H) in the list. Find typical interatomic distances for the hydrogen bonds O-H…O. What range do they vary in? (see the values of R in Å)
3. Find all contacts H…O corresponding to Van der Waals bonding. What are their distances?
4. Remove all the "non H" H…O contacts using local menu (Delete Selected or Change Type/No bond commands). Save the changes. Pay attention that the Reference Code field contains the Collection Code of the structure in ICSD.
5. Open a Crystal Data window for a lithium sulfate hydrate without allocated hydrogen atoms. Look at the typical interatomic distances corresponding to O…O hydrogen bonds. For example, compound with Ref. Code 18173 shows O1…O5 2.870 Å vdW
6. If instead of going on Change Type (step 4 above) you click on Information, you will get, e.g. for structures 22347 (with H, left) and 18173 (without H, right) the following self-explanatory windows:
 22347 |
 18173 |
Exercise:
Perform the algorithm for lithium selenate hydrates. Are there any differences in interatomic distances O…O for hydrogen bonds in lithium sulfate and selenate hydrates?
Answer:
The distances O…O for hydrogen bonds in lithium selenate is 2.87 Å 3.00-2.881 Å are typical ranges for O…O distances in hydrogen bonds in lithium sulfate.
